Positional cloning has helped identify the molecular causes of many of Mendelian disorders. Genes involved in the more common forms of deafness and ataxia have been identified and are often clinically tested. However, the cause of most genetically rare forms is still unknown because such families are often too small to provide by themselves sufficient statistical power to unambiguously identify linkage. In addition, even if families are large enough to identify a linked locus, the regions are typically so large that hundreds of genes are implicated. In some situations, linkage disequilibrium analysis can further narrow a region. Recently, global analysis of gene expression has become a reality. We hypothesize that a subset of mutated genes directly or indirectly leads to abnormal expression levels, and can be identified by combining genetic analysis with gene expression analysis of mRNA from lymphoblastoid cell lines (LCLs). Using such a combined approach, a novel epilepsy gene was recently identified in only three affected subjects. We have recently identified a novel auditory neuropathy gene, and have encouraging data for identification of a second novel deafness gene and for several novel ataxia genes. In this pilot/feasibility R21 grant, we will explore the generalizability of this approach in several families with unidentified causes of deafness or ataxia. We will perform genetic linkage, linkage disequilibrium and global gene expression analysis. Candidates genes will be identified as the intercept between genes in linkage regions and those that show significant expression changes. Computational approaches to define the intersect between genetic and gene expression data will be developed, implemented and tested. While in some cases combining genetic linkage and linkage disequilibrium with global gene expression analysis may directly identify the mutant gene, in other cases the mutation may result in functional differences in a pathway without affecting the expression of its own gene directly. In that case, more complex analysis of affected gene expression changes downstream of a mutant gene will be necessary to identify the deficient pathway and the mutation. Pathways from expression analysis, animal models and the literature and public bioinformatic databases will be used for this purpose. Candidate genes emerging from these approaches will be sequenced to identify variants, and potential mutations tested in unrelated controls. PUBLIC HEALTH RELEVANCE: The genetic cause of many forms of deafness or ataxia is still unknown. Our research will result in the identification of new genes and metabolic pathways involved in these disorders. These findings can improve accurate diagnosis, presymptomatic testing, family planning and personalizing treatment. It may also ultimately lead to new treatments.